Multiple Sclerosis (MS) is an inflammatory, demyelinating disorder of the central nervous system (CNS). The etiology of MS remains unclear, but the disease develops in genetically susceptible individuals exposed to environmental triggers. The long-favored hypothesis in MS implicates autoreactive T and B cells generated in the periphery that access the CNS, where they induce injury of previously normal neural tissues. However, in contrast to the animal model experimental autoimmune encephalomyelitis (EAE), neither the target(s) of the immune response nor the cells responsible for CNS damage have been unequivocally defined in MS. Furthermore, the failure of some MS disease modifying treatments (DMTs) that target processes underlying the development of CNS tissue destruction in EAE (e.g. IFN-g, TNF-a inhibitors) indicates that different mechanisms may cause the development of disability in MS versus EAE. Therefore, there is a need to identify pathophysiological mechanisms that are specific for MS, but may not be predicted from EAE models. Therapeutic trials, especially those that investigate novel therapeutic agents, represent a unique opportunity to investigate how specific perturbations of the biological system affect MS disease process. The goal of this project is to carefully study the biological perturbations induced by the application of novel therapeutic agents in Phase I/II clinical trials in MS, to define mechanisms of CNS tissue injury, but also those that underlie beneficial immunoregulation and immune-mediated neuroprotection. By correlating changes measured in the biological system with structural changes of CNS destruction (measured by neuroimaging), and with novel, more sensitive clinical and functional outcomes, we can understand which biological processes are beneficial and which are harmful in the MS pathogenesis. Additionally, understanding which effects of applied therapies underlie their therapeutic benefit will allow us to define biomarkers that are indicative, and ideally also predictive of the full therapeutic response. Finally, we also believe that analogously to cardiovascular, infectious diseases or oncology, successful treatment of fully evolved CNS disorder will require rational, patient-specific combination treatments that target all pathogenic mechanism responsible for his/her disease expression. This project is an extension of the NS003055: Comprehensive multimodal analysis of patients with neuroimmunological diseases project, in that it tests hypotheses derived from the NS003055 project in interventional, investigator-initiated clinical trials. We are currently finishing the investigator-initiated Phase I/II clinical trial performed under Investigational New Drug (IND) application: protocol 13-N-0088 (Open label extension trial of Idebenone for Primary Progressive Multiple Sclerosis - IPPOMS-E trial; clinicaltrials.gov identifier NCT01854359). This trial studies mitochondrial hypothesis of disability progression in primary progressive MS (PPMS). PPMS is resistant to therapy by immunomodulatory agents. Mitochondrial dysfunction coupled with oxidative stress has been proposed as one of the top alternative hypotheses underlying pathophysiology of PP-MS. Idebenone is a synthetic analogue of coenzyme-Q with lower lipophilicity, which allows its reduction by cytosolic enzymes that are upregulated under oxidative stress, such as NQO1. As such, it can improve mitochondrial metabolism under conditions with dysfunctional electron transport chain (ETC) complex I, such as Lebers hereditary optic neuropathy. Therefore, in IPPOMS-E trial, we test the hypothesis that mitochondrial dysfunction contributes to development of neurological disability in PPMS. Associated biomarker studies strive to derive and validate biomarkers of mitochondrial dysfunction in MS, as well as biomarkers of MS disease progression and severity. In 2017 we opened new Phase II clinical trial called TRAP-MS: Targeting Residual Activity by Precision, biomarker-guided combination therapies of Multiple Sclerosis (protocol 17-N-0083; clinicaltrials.gov identifier NCT03109288). TRAP-MS trial tests hypotheses derived from the knowledge we acquired in the past 5 years under project NS003055: Comprehensive multimodal analysis of patients with neuroimmunological diseases about residual MS activity when patients are treated with current FDA-approved DMTs and about pathogenic processes associated with disease progression and disease severity in MS. Specifically TRAP-MS trial tests following hypotheses: 1. Large proportion of MS patients treated with currently-approved DMTs retain measurable inflammation that is compartmentalized to the CNS tissue and consists of terminally-differentiated (and therefore largely non-proliferating) immune cells. This inflammation contributes to CNS tissue destruction and may be limited by hydroxychloroquine, which limits antigen-processing/presentation and perforin-mediated cytotoxicity. 2. Chronic intrathecal inflammation leads to activation and reprogramming of the innate immunity, especially myeloid lineage, which contributes to CNS tissue destruction and accumulation of disability. This inappropriate activation of myeloid lineage (microglia, macrophages and myeloid dendritic cells) may be inhibited by drugs pioglitazone and montelukast. 3. MS progression is also associated with inappropriate activation of endothelial cells and components of the blood brain barrier (BBB) and neurovascular unit, which leads to remodeling of the extracellular matrix that also contributes to accumulation of disability. This biology may be affected by drug losartan. 4. Afore-mentioned processes are differentially expressed in individual patients and can be measured by cerebrospinal fluid (CSF) biomarkers. Therefore, CSF biomarkers may guide selection of optimal therapy and reflect its efficacy on residual MS activity. 5. To achieve high level of efficacy (ideally complete inhibition of MS progression) patients will need combination treatments that target all pathogenic mechanisms that are active in patients CNS. We expect that biomarker and mechanistic studies that accompany TRAP-MS trial will provide missing knowledge necessary for application of precision neurology in broad MS practice. We expect that not all drugs selected for initial testing in TRAP-MS trial will prove their desired efficacy in the intrathecal compartment and this protocol includes stopping criteria for individual drugs and their future replenishment with other candidate agents.